Mercurial > repos > romaingred > pirna_pipeline

diff bin/piPipe.pl @ 31:241aa6141cac draft

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Uploaded
author romaingred
date Tue, 28 Nov 2017 08:54:52 -0500
parents 0a47c6cf912d
children 46d7549c1a05
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line diff
--- a/bin/piPipe.pl	Tue Nov 28 08:54:34 2017 -0500
+++ b/bin/piPipe.pl	Tue Nov 28 08:54:52 2017 -0500
@@ -245,8 +245,8 @@
 	if ( $Pcheck eq 'true' )
 	{
 		my $ppp = $group_dir.'PPPartners/'; mkdir $ppp;
-		print $report "ping_pong_partners $group_dir/bonafide_reads/TEs.sam $ppp\n";
-		ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'bonafide_reads/bonafide_reads-TEs_sorted.bam', $ppp, $min );
+		print $report "ping_pong_partners $group_dir/piRNAs/TEs.sam $ppp\n";
+		ping_pong_partners ( $group_dir.'TEs.fai', $group_dir.'piRNAs/piRNAs-TEs_sorted.bam', $ppp, $pi_min );
 		my $ppp_page = $dir.$fastq_n[$child].'-bonafide_reads-PPP.html';
 		ppp_page ( $group_dir, $ppp_page, \@fastq_n, $fastq_n[$child], $ppp, $dir );
 	}